Create figures for CyTOF myeloid panel data. Preprocessing and preliminary analysis were done by Dimitrios N. Sidiropoulos.
##
## Baseline C1D1 C2D1
## 28 28 8
## The number of paired samples between Baseline and C1D1: 28
## The number of paired samples between Baseline and C2D1: 8
## The number of paired samples between C2D1 and C1D1: 8
P-values from paired two-sided Wilcoxon test between time points and mean of difference between time points
| pValue_BvsC1D1 | mean(C1D1-B) | pValue_C1D1vsC2D1 | mean(C2D1-C1D1) | pValue_BvsC2D2 | mean(C2D1-B) | |
|---|---|---|---|---|---|---|
| B | 0.000 | -1.399 | 0.023 | -1.174 | 0.008 | -2.674 |
| cDC1 | 0.479 | -0.078 | 0.109 | 0.712 | 0.250 | 0.894 |
| cDC2 | 0.000 | -0.263 | 0.844 | -0.059 | 0.109 | -0.436 |
| DNT | 0.008 | -0.247 | 0.547 | -0.157 | 0.109 | -0.235 |
| Early Myelocyte | 0.001 | -1.085 | 0.844 | 0.703 | 0.383 | -0.112 |
| Granulocytes | 0.937 | -0.006 | 0.109 | -0.007 | 0.078 | -0.004 |
| Non-Classical Mono | 0.264 | -0.394 | 0.844 | 0.746 | 0.742 | -0.324 |
| pDC | 0.000 | -0.461 | 0.547 | 0.122 | 0.547 | -0.152 |
| preDC/Classical Mono | 0.007 | 8.032 | 0.313 | 6.048 | 0.016 | 16.117 |
| Tc | 0.662 | -0.525 | 0.023 | -2.823 | 0.008 | -2.930 |
| Th | 0.090 | -3.574 | 0.250 | -4.110 | 0.008 | -10.144 |
## [1] "Significant change (p-value < 0.05) in proportions of cells in the following cell types:"
## $pValue_BvsC1D1
## [1] "B" "cDC2" "DNT"
## [4] "Early Myelocyte" "pDC" "preDC/Classical Mono"
##
## $pValue_C1D1vsC2D1
## [1] "B" "Tc"
##
## $pValue_BvsC2D2
## [1] "B" "preDC/Classical Mono" "Tc"
## [4] "Th"
For significant cell types only
## [1] "The number of pairs (cluster, marker) with significant change (p-value < 0.05) in marker expression between baseline and C1D1:"
## [1] 152
## [1] "CD19 in B"
## [1] "CD117 in B"
## [1] "CD11B in B"
## [1] "CD1C in B"
## [1] "CCR2 in B"
## [1] "CD123 in B"
## [1] "CLEC9A in B"
## [1] "CD11C in B"
## [1] "CD141 in B"
## [1] "CD80 in B"
## [1] "TLR4 in B"
## [1] "CD172AB in B"
## [1] "CD40 in B"
## [1] "CD206 in B"
## [1] "HLADR in B"
## [1] "CD68 in B"
## [1] "PDL1 in B"
## [1] "CD3 in cDC1"
## [1] "CD11B in cDC1"
## [1] "CD4 in cDC1"
## [1] "CD8 in cDC1"
## [1] "CXCR2 in cDC1"
## [1] "CD1C in cDC1"
## [1] "FCERI in cDC1"
## [1] "CCR5 in cDC1"
## [1] "CLEC9A in cDC1"
## [1] "CD11C in cDC1"
## [1] "TLR4 in cDC1"
## [1] "CD40 in cDC1"
## [1] "CD206 in cDC1"
## [1] "CD33 in cDC1"
## [1] "CD68 in cDC1"
## [1] "CD116 in cDC1"
## [1] "PDL1 in cDC1"
## [1] "CD135 in cDC1"
## [1] "CD117 in cDC2"
## [1] "CD11B in cDC2"
## [1] "CD4 in cDC2"
## [1] "CD14 in cDC2"
## [1] "FCERI in cDC2"
## [1] "CD103 in cDC2"
## [1] "CCR2 in cDC2"
## [1] "CD123 in cDC2"
## [1] "CCR5 in cDC2"
## [1] "CD11C in cDC2"
## [1] "TLR4 in cDC2"
## [1] "CD172AB in cDC2"
## [1] "CD40 in cDC2"
## [1] "PDL2 in cDC2"
## [1] "CCR7 in cDC2"
## [1] "CD206 in cDC2"
## [1] "HLADR in cDC2"
## [1] "CD68 in cDC2"
## [1] "CD15 in cDC2"
## [1] "PDL1 in cDC2"
## [1] "CD16 in cDC2"
## [1] "Arg1 in cDC2"
## [1] "CD8 in DNT"
## [1] "CD163 in DNT"
## [1] "CLEC9A in DNT"
## [1] "CD11C in DNT"
## [1] "CD172AB in DNT"
## [1] "PDL2 in DNT"
## [1] "CCR7 in DNT"
## [1] "HLADR in DNT"
## [1] "PDL1 in DNT"
## [1] "CD3 in Early Myelocyte"
## [1] "CD4 in Early Myelocyte"
## [1] "CD8 in Early Myelocyte"
## [1] "CXCR2 in Early Myelocyte"
## [1] "CD66B in Early Myelocyte"
## [1] "CCR2 in Early Myelocyte"
## [1] "CCR5 in Early Myelocyte"
## [1] "CD11C in Early Myelocyte"
## [1] "CD141 in Early Myelocyte"
## [1] "CD40 in Early Myelocyte"
## [1] "PDL1 in Early Myelocyte"
## [1] "CD135 in Early Myelocyte"
## [1] "CD16 in Early Myelocyte"
## [1] "CCR5 in Granulocytes"
## [1] "CXCR4 in Granulocytes"
## [1] "CD4 in Non-Classical Mono"
## [1] "CD8 in Non-Classical Mono"
## [1] "CD14 in Non-Classical Mono"
## [1] "CD1C in Non-Classical Mono"
## [1] "FCERI in Non-Classical Mono"
## [1] "CCR2 in Non-Classical Mono"
## [1] "CD123 in Non-Classical Mono"
## [1] "CCR5 in Non-Classical Mono"
## [1] "CLEC9A in Non-Classical Mono"
## [1] "CD11C in Non-Classical Mono"
## [1] "CD141 in Non-Classical Mono"
## [1] "CD80 in Non-Classical Mono"
## [1] "CCR7 in Non-Classical Mono"
## [1] "CD33 in Non-Classical Mono"
## [1] "CD68 in Non-Classical Mono"
## [1] "CD116 in Non-Classical Mono"
## [1] "PDL1 in Non-Classical Mono"
## [1] "CD135 in Non-Classical Mono"
## [1] "CD16 in Non-Classical Mono"
## [1] "Arg1 in Non-Classical Mono"
## [1] "CD19 in pDC"
## [1] "CD4 in pDC"
## [1] "CCR2 in pDC"
## [1] "CD123 in pDC"
## [1] "TLR4 in pDC"
## [1] "CD172AB in pDC"
## [1] "CD40 in pDC"
## [1] "CD206 in pDC"
## [1] "CD33 in pDC"
## [1] "CD16 in pDC"
## [1] "CD19 in preDC/Classical Mono"
## [1] "CD117 in preDC/Classical Mono"
## [1] "CD11B in preDC/Classical Mono"
## [1] "CD14 in preDC/Classical Mono"
## [1] "CD66B in preDC/Classical Mono"
## [1] "CCR5 in preDC/Classical Mono"
## [1] "CD11C in preDC/Classical Mono"
## [1] "TLR4 in preDC/Classical Mono"
## [1] "CD172AB in preDC/Classical Mono"
## [1] "CD40 in preDC/Classical Mono"
## [1] "PDL2 in preDC/Classical Mono"
## [1] "CD206 in preDC/Classical Mono"
## [1] "PDL1 in preDC/Classical Mono"
## [1] "Arg1 in preDC/Classical Mono"
## [1] "CD1C in Tc"
## [1] "CCR2 in Tc"
## [1] "CD123 in Tc"
## [1] "CCR5 in Tc"
## [1] "CD11C in Tc"
## [1] "CD80 in Tc"
## [1] "CD172AB in Tc"
## [1] "CD33 in Tc"
## [1] "HLADR in Tc"
## [1] "CD68 in Tc"
## [1] "CD15 in Tc"
## [1] "PDL1 in Tc"
## [1] "Arg1 in Tc"
## [1] "CD1C in Th"
## [1] "FCERI in Th"
## [1] "CCR2 in Th"
## [1] "CD123 in Th"
## [1] "CCR5 in Th"
## [1] "CD11C in Th"
## [1] "CD172AB in Th"
## [1] "CD33 in Th"
## [1] "HLADR in Th"
## [1] "CD15 in Th"
## [1] "CXCR4 in Th"
## [1] "CD116 in Th"
## [1] "PDL1 in Th"
## [1] "Arg1 in Th"
## [1] "CD19 in B"
## [1] "CD117 in B"
## [1] "CD11B in B"
## [1] "CD1C in B"
## [1] "CCR2 in B"
## [1] "CD123 in B"
## [1] "CLEC9A in B"
## [1] "CD11C in B"
## [1] "CD141 in B"
## [1] "CD80 in B"
## [1] "TLR4 in B"
## [1] "CD172AB in B"
## [1] "CD40 in B"
## [1] "CD206 in B"
## [1] "HLADR in B"
## [1] "CD68 in B"
## [1] "PDL1 in B"
## [1] "CD3 in cDC1"
## [1] "CD11B in cDC1"
## [1] "CD4 in cDC1"
## [1] "CD8 in cDC1"
## [1] "CXCR2 in cDC1"
## [1] "CD1C in cDC1"
## [1] "FCERI in cDC1"
## [1] "CCR5 in cDC1"
## [1] "CLEC9A in cDC1"
## [1] "CD11C in cDC1"
## [1] "TLR4 in cDC1"
## [1] "CD40 in cDC1"
## [1] "CD206 in cDC1"
## [1] "CD33 in cDC1"
## [1] "CD68 in cDC1"
## [1] "CD116 in cDC1"
## [1] "PDL1 in cDC1"
## [1] "CD135 in cDC1"
## [1] "CD117 in cDC2"
## [1] "CD11B in cDC2"
## [1] "CD4 in cDC2"
## [1] "CD14 in cDC2"
## [1] "FCERI in cDC2"
## [1] "CD103 in cDC2"
## [1] "CCR2 in cDC2"
## [1] "CD123 in cDC2"
## [1] "CCR5 in cDC2"
## [1] "CD11C in cDC2"
## [1] "TLR4 in cDC2"
## [1] "CD172AB in cDC2"
## [1] "CD40 in cDC2"
## [1] "PDL2 in cDC2"
## [1] "CCR7 in cDC2"
## [1] "CD206 in cDC2"
## [1] "HLADR in cDC2"
## [1] "CD68 in cDC2"
## [1] "CD15 in cDC2"
## [1] "PDL1 in cDC2"
## [1] "CD16 in cDC2"
## [1] "Arg1 in cDC2"
## [1] "CD8 in DNT"
## [1] "CD163 in DNT"
## [1] "CLEC9A in DNT"
## [1] "CD11C in DNT"
## [1] "CD172AB in DNT"
## [1] "PDL2 in DNT"
## [1] "CCR7 in DNT"
## [1] "HLADR in DNT"
## [1] "PDL1 in DNT"
## [1] "CD3 in Early Myelocyte"
## [1] "CD4 in Early Myelocyte"
## [1] "CD8 in Early Myelocyte"
## [1] "CXCR2 in Early Myelocyte"
## [1] "CD66B in Early Myelocyte"
## [1] "CCR2 in Early Myelocyte"
## [1] "CCR5 in Early Myelocyte"
## [1] "CD11C in Early Myelocyte"
## [1] "CD141 in Early Myelocyte"
## [1] "CD40 in Early Myelocyte"
## [1] "PDL1 in Early Myelocyte"
## [1] "CD135 in Early Myelocyte"
## [1] "CD16 in Early Myelocyte"
## [1] "CCR5 in Granulocytes"
## [1] "CXCR4 in Granulocytes"
## [1] "CD4 in Non-Classical Mono"
## [1] "CD8 in Non-Classical Mono"
## [1] "CD14 in Non-Classical Mono"
## [1] "CD1C in Non-Classical Mono"
## [1] "FCERI in Non-Classical Mono"
## [1] "CCR2 in Non-Classical Mono"
## [1] "CD123 in Non-Classical Mono"
## [1] "CCR5 in Non-Classical Mono"
## [1] "CLEC9A in Non-Classical Mono"
## [1] "CD11C in Non-Classical Mono"
## [1] "CD141 in Non-Classical Mono"
## [1] "CD80 in Non-Classical Mono"
## [1] "CCR7 in Non-Classical Mono"
## [1] "CD33 in Non-Classical Mono"
## [1] "CD68 in Non-Classical Mono"
## [1] "CD116 in Non-Classical Mono"
## [1] "PDL1 in Non-Classical Mono"
## [1] "CD135 in Non-Classical Mono"
## [1] "CD16 in Non-Classical Mono"
## [1] "Arg1 in Non-Classical Mono"
## [1] "CD19 in pDC"
## [1] "CD4 in pDC"
## [1] "CCR2 in pDC"
## [1] "CD123 in pDC"
## [1] "TLR4 in pDC"
## [1] "CD172AB in pDC"
## [1] "CD40 in pDC"
## [1] "CD206 in pDC"
## [1] "CD33 in pDC"
## [1] "CD16 in pDC"
## [1] "CD19 in preDC/Classical Mono"
## [1] "CD117 in preDC/Classical Mono"
## [1] "CD11B in preDC/Classical Mono"
## [1] "CD14 in preDC/Classical Mono"
## [1] "CD66B in preDC/Classical Mono"
## [1] "CCR5 in preDC/Classical Mono"
## [1] "CD11C in preDC/Classical Mono"
## [1] "TLR4 in preDC/Classical Mono"
## [1] "CD172AB in preDC/Classical Mono"
## [1] "CD40 in preDC/Classical Mono"
## [1] "PDL2 in preDC/Classical Mono"
## [1] "CD206 in preDC/Classical Mono"
## [1] "PDL1 in preDC/Classical Mono"
## [1] "Arg1 in preDC/Classical Mono"
## [1] "CD1C in Tc"
## [1] "CCR2 in Tc"
## [1] "CD123 in Tc"
## [1] "CCR5 in Tc"
## [1] "CD11C in Tc"
## [1] "CD80 in Tc"
## [1] "CD172AB in Tc"
## [1] "CD33 in Tc"
## [1] "HLADR in Tc"
## [1] "CD68 in Tc"
## [1] "CD15 in Tc"
## [1] "PDL1 in Tc"
## [1] "Arg1 in Tc"
## [1] "CD1C in Th"
## [1] "FCERI in Th"
## [1] "CCR2 in Th"
## [1] "CD123 in Th"
## [1] "CCR5 in Th"
## [1] "CD11C in Th"
## [1] "CD172AB in Th"
## [1] "CD33 in Th"
## [1] "HLADR in Th"
## [1] "CD15 in Th"
## [1] "CXCR4 in Th"
## [1] "CD116 in Th"
## [1] "PDL1 in Th"
## [1] "Arg1 in Th"
## R version 4.3.2 (2023-10-31 ucrt)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 19045)
##
## Matrix products: default
##
##
## locale:
## [1] LC_COLLATE=English_United States.utf8
## [2] LC_CTYPE=English_United States.utf8
## [3] LC_MONETARY=English_United States.utf8
## [4] LC_NUMERIC=C
## [5] LC_TIME=English_United States.utf8
##
## time zone: America/New_York
## tzcode source: internal
##
## attached base packages:
## [1] grid stats4 stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] ashr_2.2-63 pheatmap_1.0.12
## [3] scales_1.3.0 Matrix_1.6-3
## [5] data.table_1.14.8 BiocManager_1.30.22
## [7] survival_3.5-7 binom_1.1-1.1
## [9] flextable_0.9.4 survminer_0.4.9
## [11] msigdbr_7.5.1 fgsea_1.26.0
## [13] EnhancedVolcano_1.18.0 ComplexHeatmap_2.16.0
## [15] DESeq2_1.40.2 SummarizedExperiment_1.30.2
## [17] Biobase_2.60.0 MatrixGenerics_1.12.3
## [19] matrixStats_1.1.0 GenomicRanges_1.52.1
## [21] GenomeInfoDb_1.36.4 IRanges_2.34.1
## [23] S4Vectors_0.38.2 BiocGenerics_0.46.0
## [25] kableExtra_1.3.4 pals_1.8
## [27] gridExtra_2.3 DT_0.30
## [29] ggrepel_0.9.4 ggpubr_0.6.0
## [31] ggplot2_3.4.4 dplyr_1.1.2
## [33] knitr_1.45
##
## loaded via a namespace (and not attached):
## [1] splines_4.3.2 later_1.3.1 bitops_1.0-7
## [4] tibble_3.2.1 lifecycle_1.0.4 rstatix_0.7.2
## [7] mixsqp_0.3-54 doParallel_1.0.17 lattice_0.21-9
## [10] crosstalk_1.2.1 backports_1.4.1 magrittr_2.0.3
## [13] sass_0.4.8 rmarkdown_2.25 jquerylib_0.1.4
## [16] yaml_2.3.7 httpuv_1.6.12 zip_2.3.0
## [19] askpass_1.2.0 cowplot_1.1.2 mapproj_1.2.11
## [22] RColorBrewer_1.1-3 maps_3.4.1.1 abind_1.4-5
## [25] zlibbioc_1.46.0 rvest_1.0.3 purrr_1.0.2
## [28] RCurl_1.98-1.13 gdtools_0.3.4 circlize_0.4.15
## [31] GenomeInfoDbData_1.2.10 KMsurv_0.1-5 irlba_2.3.5.1
## [34] crul_1.4.0 svglite_2.1.2 commonmark_1.9.0
## [37] codetools_0.2-19 DelayedArray_0.26.7 ggtext_0.1.2
## [40] xml2_1.3.5 tidyselect_1.2.0 shape_1.4.6
## [43] httpcode_0.3.0 farver_2.1.1 webshot_0.5.5
## [46] jsonlite_1.8.7 GetoptLong_1.0.5 ellipsis_0.3.2
## [49] iterators_1.0.14 systemfonts_1.0.5 foreach_1.5.2
## [52] tools_4.3.2 ragg_1.2.6 snow_0.4-4
## [55] Rcpp_1.0.11 glue_1.6.2 xfun_0.39
## [58] withr_2.5.2 fastmap_1.1.1 fansi_1.0.4
## [61] openssl_2.1.1 digest_0.6.33 truncnorm_1.0-9
## [64] R6_2.5.1 mime_0.12 textshaping_0.3.7
## [67] colorspace_2.1-0 dichromat_2.0-0.1 markdown_1.12
## [70] utf8_1.2.3 tidyr_1.3.0 generics_0.1.3
## [73] fontLiberation_0.1.0 httr_1.4.7 htmlwidgets_1.6.4
## [76] S4Arrays_1.0.6 pkgconfig_2.0.3 gtable_0.3.4
## [79] XVector_0.40.0 survMisc_0.5.6 htmltools_0.5.7
## [82] fontBitstreamVera_0.1.1 carData_3.0-5 clue_0.3-65
## [85] png_0.1-8 km.ci_0.5-6 rstudioapi_0.15.0
## [88] reshape2_1.4.4 rjson_0.2.21 uuid_1.1-1
## [91] curl_5.1.0 zoo_1.8-12 cachem_1.0.8
## [94] GlobalOptions_0.1.2 stringr_1.5.1 parallel_4.3.2
## [97] pillar_1.9.0 vctrs_0.6.3 promises_1.2.1
## [100] car_3.1-2 xtable_1.8-4 cluster_2.1.4
## [103] evaluate_0.23 invgamma_1.1 cli_3.6.1
## [106] locfit_1.5-9.8 compiler_4.3.2 rlang_1.1.1
## [109] crayon_1.5.2 SQUAREM_2021.1 ggsignif_0.6.4
## [112] labeling_0.4.3 plyr_1.8.9 stringi_1.8.1
## [115] viridisLite_0.4.2 BiocParallel_1.34.2 babelgene_22.9
## [118] munsell_0.5.0 fontquiver_0.2.1 gfonts_0.2.0
## [121] shiny_1.8.0 highr_0.10 gridtext_0.1.5
## [124] broom_1.0.5 bslib_0.6.1 fastmatch_1.1-4
## [127] officer_0.6.3